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Quantifying Mineral-Ligand Structural Similarities: Bridging the Geological World of Minerals with the Biological World of Enzymes

Zhao, Daniel and Bartlett, Stuart and Yung, Yuk L. (2020) Quantifying Mineral-Ligand Structural Similarities: Bridging the Geological World of Minerals with the Biological World of Enzymes. Life, 10 (12). Art. No. 338. ISSN 2075-1729. PMCID PMC7764262. doi:10.3390/life10120338.

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Metal compounds abundant on Early Earth are thought to play an important role in the origins of life. Certain iron-sulfur minerals for example, are proposed to have served as primitive metalloenzyme cofactors due to their ability to catalyze organic synthesis processes and facilitate electron transfer reactions. An inherent difficulty with studying the catalytic potential of many metal compounds is the wide range of data and parameters to consider when searching for individual minerals and ligands of interest. Detecting mineral-ligand pairs that are structurally analogous enables more relevant selections of data to study, since structural affinity is a key indicator of comparable catalytic function. However, current structure-oriented approaches tend to be subjective and localized, and do not quantify observations or compare them with other potential targets. Here, we present a mathematical approach that compares structural similarities between various minerals and ligands using molecular similarity metrics. We use an iterative substructure search in the crystal lattice, paired with benchmark structural similarity methods. This structural comparison may be considered as a first stage in a more advanced analysis tool that will include a range of chemical and physical factors when computing mineral-ligand similarity. This approach will seek relationships between the mineral and enzyme worlds, with applications to the origins of life, ecology, catalysis, and astrobiology.

Item Type:Article
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URLURL TypeDescription CentralArticle
Bartlett, Stuart0000-0001-5680-476X
Yung, Yuk L.0000-0002-4263-2562
Additional Information:© 2020 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license ( Received: 14 September 2020 / Revised: 15 November 2020 / Accepted: 7 December 2020 / Published: 10 December 2020. (This article belongs to the Special Issue From Messy Chemistry to the Origin of Life) We wish to thank Yamei Li of the Earth-Life Science Institute for invaluable advice and help during this work. We also wish to thank Michael Russell for his assistance and feedback, Hyman Hartman and Michael Wong for inspiring discussions, and the Caltech GPS ‘Astrobiothermoevo’ reading group. We gratefully acknowledge the feedback of four reviewers. This work was supported by the Caltech Division of Geological and Planetary Sciences Discovery Fund. Y.L.Y. was supported in part by an NAI Virtual Planetary Laboratory grant from the University of Washington to the Jet Propulsion Laboratory and California Institute of Technology. Author Contributions. S.B. conceived the idea of applying a big data, structural comparison of minerals and enzyme ligands, and provided guidance to D.Z., who sourced the mineral and ligand structures, designed the crystal structure manipulation method, performed the analysis and structure comparisons, produced the figures and wrote most of the text. Y.L.Y. provided guidance and assistance throughout the project. All authors have read and agreed to the published version of the manuscript. The authors declare no conflict of interest.
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Caltech Division of Geological and Planetary SciencesUNSPECIFIED
Subject Keywords:origin of life; minerals; enzymes; ligand; astrobiology
Issue or Number:12
PubMed Central ID:PMC7764262
Record Number:CaltechAUTHORS:20201215-141036988
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Official Citation:Zhao, D.; Bartlett, S.; Yung, Y.L. Quantifying Mineral-Ligand Structural Similarities: Bridging the Geological World of Minerals with the Biological World of Enzymes. Life 2020, 10, 338.
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:107094
Deposited By: George Porter
Deposited On:16 Dec 2020 18:48
Last Modified:16 Nov 2021 18:59

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